I think part of the problem here is that the core mechanic to Zoe's W is not innately designed to scale. The ability lets you copy item actives and summoner spells, neither of which have ranks, the activation comes from charges, which have a fixed cooldown, and the active itself has no innate cooldown or mana cost. There are effectively no innate balancing levers to such an ability, which is why it got a pseudo-Ahri W tacked onto it.
Personally, to me this is just one more reason why Spell Thief should be Zoe's ultimate, and Portal Jump her W. As a basic ability, Spell Thief has had a ton of problems, namely because a lot of item actives aren't meant to be used so early in the game, and free item actives and summoner spells have a disproportionately large impact in the early game, especially those with global or semi-global range. On top of that, it's currently loaded with an effect that is neither unique nor interesting, that Zoe could easily stand to lose. Meanwhile, Portal Jump is an essential component to Zoe's combos, and can be much more easily tuned to be reasonable in lane, especially since it doesn't allow her to reposition. In fact, giving Zoe exactly one rank in her ult, and the rest to her basic abilities, could allow her damage to progress much more smoothly overall, particularly since her Q tends to spike really hard due to the way her damage works.